Boyes was drafted by the Toronto Maple Leafs in the first round, 24th overall in the 2000 NHL Entry Draft.
He was traded to the San Jose Sharks along with Alyn McCauley and a 1st round selection in the 2003 NHL Entry Draft (who would be Mark Stuart) in exchange for Owen Nolan.
Boyes was later traded from the Sharks to the Boston Bruins in a 3-way deal that saw Jeff Jillson go to Buffalo Sabres, Curtis Brown go to San Jose, and Brad Boyes and Andy Delmore go to Boston on March 9, 2004.
Boyes scored his first NHL goal on October 9, 2005 against Sébastien Caron of the Pittsburgh Penguins. He scored his first NHL hat trick on March 18, 2006 against Cam Ward of the Carolina Hurricanes.